Here's my server's Starbound related config files and scripts.

bash_aliases.sh

alias sb_start="sudo start starbound"
alias sb_stop="sudo stop starbound"
alias sb_restart="sb_stop;sb_start"
alias sb_update="sudo /home/ribesg/sb_update"
alias sb_online="netstat -nt | grep -c 21025"
alias sb_status="sudo status starbound"

sb_update.sh

#!/bin/bash

###########################
## Default Configuration ##
###########################

# STEAM_USER - The Steam or Starbound unix user, whatever you named it
STEAM_USER="steam"

# STARBOUND_FOLDER - The root starbound folder
# WARNING: THIS SCRIPT ERASE THIS FOLDER - DOUBLE CHECK IT!
STARBOUND_FOLDER="/home/$STEAM_USER/starbound"

# TO_BACKUP_FOLDER - Should contain the folder to backup
# You can use the linuxXX folder or the whole starbound folder, or just the universe folder
TO_BACKUP_FOLDER="/home/$STEAM_USER/starbound/universe"

# DEST_FILE - The destination file for backup
# I use the date in it, but you can do whatever you want
DATE=$(date +%F_%H:%M:%S)
DEST_FILE="/home/$STEAM_USER/backups/universe-$DATE.tar.bzip2"

# STEAM_CMD - Location of the steamcmd.sh script
STEAM_CMD="/home/$STEAM_USER/steamcmd.sh"

# STEAM_LOGIN - Do I need to define what it is
STEAM_LOGIN="YourSteamLogin"

# STEAM_PASSWORD - In the futur we should be able to use anonymous Steam login...
STEAM_PASSWORD="YourSteamPassword"

# SERVER_PASSWORD - The password to apply to the server
# Note: Setting this to empty will apply an empty password, aka no password
SERVER_PASSWORD="YourServerPassword"

#
# Arguments that can be changed by command line
#

# Will be set to true if argument passed is "clean" 
CLEAN=false
if [[ "$1" == "clean" || "$2" == "clean" ]]; then
	CLEAN=true
	echo "Clean set to true"
fi

# Will be set to true if argument passed is "nobackup"
NOBACKUP=false
if [[ "$1" == "nobackup" || "$2" == "nobackup" ]]; then
	NOBACKUP=true
	echo "Nobackup set to true"
fi

############
## Script ##
############

echo "###############################"
echo "## Updating Starbound Server ##"
echo "###############################"

RESTART=false

# Check server status and shut it down if it's online
echo
echo "1 - Checking server status..."
STATUS=$(sudo initctl status starbound)
echo "Status: $STATUS"
if [[ "$STATUS" =~ ^(.*)start(.*)$ ]]; then
	echo "Server is online! Shutting down..."
	sudo initctl stop starbound >/dev/null 2>&1
	echo "Server shut down!"
	RESTART=true
else
	echo "Server is offline!"
fi
echo "1 - Done!"

# Backup the whole server, just in case
echo
echo "2 - Make a backup of the $TO_BACKUP_FOLDER folder"
if $NOBACKUP; then
	echo "2 - Skipped!"
elif [ ! -d "$TO_BACKUP_FOLDER" ]; then
	echo "2 - Not found!"
else
	echo "Compressing $(sudo find $TO_BACKUP_FOLDER/* -type f | wc -l) files..."
	sudo tar cf - $TO_BACKUP_FOLDER -P | sudo pv -w 80 -s $(sudo du -sb $TO_BACKUP_FOLDER | sudo awk '{print $1}') | sudo bzip2 > $DEST_FILE
	sudo chown $STEAM_USER:$STEAM_USER $DEST_FILE
	echo "2 - Done!"
fi

# Remove the existing starbound folder
echo
echo "3 - Remove the 'old' starbound folder $STARBOUND_FOLDER"
if $CLEAN; then
	echo "Removing..."
	sudo rm -rf $STARBOUND_FOLDER
	echo "3 - Done!"
else
	echo "3 - Skipped!"
fi

# Use SteamCMD to re-download the up-to-date server
echo
echo "4 - Update the server using SteamCMD"
echo "Calling $STEAM_CMD..."
sudo su $STEAM_USER -c "$STEAM_CMD +login $STEAM_LOGIN $STEAM_PASSWORD +force_install_dir $STARBOUND_FOLDER +app_update 211820 validate +quit"
echo "4 - Done!"

# Start the server to generate the config file
echo
echo "5 - Starting server to generate config file"
echo "Starting..."
sudo initctl start starbound >/dev/null 2>&1
echo "Waiting some seconds..."
sleep 1
echo "10..."
sleep 1
echo " 9..."
sleep 1
echo " 8..."
sleep 1
echo " 7..."
sleep 1
echo " 6..."
sleep 1
echo " 5..."
sleep 1
echo " 4..."
sleep 1
echo " 3..."
sleep 1
echo " 2..."
sleep 1
echo " 1..."
sleep 1
echo " 0!"
echo "Shutting down server..."
sudo initctl stop starbound >/dev/null 2>&1
echo "Server shut down!"


# Set password in config
CONFIG_FILE="$STARBOUND_FOLDER/starbound.config"
echo
echo "6 - Setting password in $CONFIG_FILE"
echo "Replacing..."
sudo su $STEAM_USER -c "mv $CONFIG_FILE $CONFIG_FILE.tmp"
sudo su $STEAM_USER -c "cat $CONFIG_FILE.tmp | jq '.serverPasswords = [ \"$SERVER_PASSWORD\" ]' > $CONFIG_FILE"
echo "6 - Done!"

# If the server was on, restart it
if $RESTART; then
	echo
	echo "7 - The server was online, restart it"
	echo "Restarting..."
	sudo initctl start starbound >/dev/null 2>&1
	echo "7 - Done!"
else
	echo
	echo "7 - The server was offline, we do not restart it"
fi

echo
echo "######################################"
echo "## Starbound Server update Complete ##"
echo "######################################"

starbound.conf.sh

#!upstart
description "Starbound"

# As Steam user
setuid steam

# Start the job
exec '/home/steam/starbound/linux64/starbound_server'

# Start on boot (when Disk + Network OK)
start on filesystem and net-device-up IFACE=lo

# Restart the process if it dies
respawn

# Give up if restart occurs 10 times in 90 seconds
respawn limit 10 90

I added ".sh" to all files to force Github to colorize them correctly.

• .bash_aliases contains some aliases I use as my server's main unix user
• starbound.conf is an Upstart script that will handle the server's status and ease the start/stop/restart processes
• sb_update is a script I made to update my Starbound server. It allows:
  • Automatically stops the server if needed
  • Make a backup of a predefined folder (in this case the universe folder), unless you call it with the argument "nobackup"
  • Remove the starbound folder if the argument "clean" is passed (good for clean reinstall)
  • Launch SteamCMD to re-download the game
  • Modify the "assets/default_configuration.config" file to set the server's password
  • Restart the server if it was online when the script was launched

Full list of required commands: date, sudo, initctl (Upstart), find, wc, tar, pv, du, awk, bzip2, chown, rm, su, mv, cat, jq (http://stedolan.github.io/jq/).

Please comment here for additional informations.

Updated for v. Furious Koala

thanks for the great update script!